Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crosslinking mass spectrometry dataset for mzIdentML 1.3 validation with MeroX 2.0.2.5

ABSTRACT: This dataset was generated to support the validation of mzIdentML 1.3 files, including the crosslinking extension. The dataset contains LC-MS/MS data and crosslinking search results for DSBU-crosslinked peptides, together with mzIdentML 1.3 files containing crosslinking-specific annotations and controlled vocabulary terms.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Alice Vetrano

LAB HEAD: Claudio Iacobucci

PROVIDER: PXD077188 | Pride | 2026-06-03

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LH3_GLT.fasta	Fasta
	LH3_W158R.mgf	Mgf
	LH3_W158R.mzid	Mzid
	LH3_W158R.zhrm	Other
	LH3_W158_R_9_GB6_1_2911.d.zip	Other

Items per page:

1 - 5 of 7

Similar Datasets

ProteomeDiscover Crosslinking Complete Submission - HEK 293 XL fractions analysis

Project description:The following dataset is an example and gold-standard dataset of a Crosslinking (XL) Complete submission to PRIDE Archive using mzIdentML and the guidelines for XL submissions. The dataset is a HEK 293 sample analyzed with multiple fractions.

2025-01-16 | PXD059766 | Pride

ABRF iPRG 2023 crosslinking study - Kojak COMPLETE results

Project description:The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year (2023) the iPRG group has put together a crosslinking study. The goal is to teach people how to analyze crosslinked samples with existing software and provide them with data sets that they can practice on. It is then hoped that more core labs will offer crosslinking analysis as a service to customers and collaborators. This particular submission provides the Kojak results in COMPLETE dataset format supporting mzIdentML 1.2.0 and it is used as a gold-standard for the new PRIDE Archive resource https://www.ebi.ac.uk/pride/archive/crosslinking

2024-10-17 | PXD056910 | Pride

Determination of protein monoclonal-antibody epitopes by a combination of structural proteomics methods.

Project description:We use a combination of multiple structural proteomics techniques (differential photo-reactive surface modification, HDX, crosslinking and epitope excision/extraction) for the determination of the protein antigen epitopes for monoclonal antibodies.

2023-10-24 | PXD040902 | Pride

Integrative structural analysis of NF90-NF45 heterodimers reveals architectural rearrangements and oligomerisation on binding dsRNA

Project description:EDC Crosslinking Mass Spectrometry with quantitation of NF90-NF45 protein complex and NF45-NF90long-dsRNA complex

2025-05-07 | PXD053010 | Pride

A synthetic crosslinked peptide library for benchmarking crosslinking mass spectrometry search engines

Project description:We have created a synthetic crosslinked peptide library to benchmark crosslinking mass spectrometry search engines. The unique benefit of the library is knowing which identified crosslinks are true and which are false. The data collected from mass spectrometry measurements of the peptide library were used to assess the most frequently used search algorithms. The datasets included will provide an important resource for the crosslinking community to evaluate and optimise search engines, results from which have far-reaching implications.

2020-07-28 | PXD014337 | Pride

ABRF iPRG 2023 crosslinking study - Mascot COMPLETE results

Project description:The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year (2023) the iPRG group has put together a crosslinking study. The goal is to teach people how to analyze crosslinked samples with existing software and provide them with data sets that they can practice on. It is then hoped that more core labs will offer crosslinking analysis as a service to customers and collaborators. This particular submission provides the Mascot results in COMPLETE dataset format supporting mzIdentML 1.2.0 and it is used as a gold-standard for the new PRIDE Archive resource https://www.ebi.ac.uk/pride/archive/crosslinking.

2024-08-08 | PXD054720 | Pride

The modulation of CHD4 nucleosome remodelling activity by auxiliary domains suggests unifies mechanistic aspects of chromatin remodelling across enzyme families

Project description:We determine the impact of auxiliary domains on the nucleosome sliding activity of CHD4. This dataset comprises the crosslinking mass spectrometry data we reported.

2023-03-11 | PXD033633 | Pride

Crosslinking MS to elucidate the Architecture of the Nucleosome Remodelling and Deacetylase (NuRD) complex

Project description:The Nucleosome Remodeling and Deacetylase (NuRD) complex is essential for development in complex animals but has been refractory to detailed analysis because of its low abundance and resistance to recombinant production. In combination with other techniques, crosslinking mass spectrometry was used to elucidate the structure of the Nucleosome Remodelling and Deacetylase (NuRD) complex. Natively-purified NuRD, and four recombinantly-expressed NuRD subcomplexes, and a PWWP2A-MTA-HDAC-RBBP alternative ‘NuRD-like’ complex were subjected to crosslinking with DSS, ADH, BS3 and DMTMM.

2021-01-08 | PXD010111 | Pride

Early Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC

Project description:In this study, NAC was UV-crosslinked using the photo-crosslinking amino acid p-benzoyl-L-phenylalanine (pBPA) in order to determine specific interaction sites of the alphaNAC N-terminus in the native protein structure. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare crosslink abundances of a NAC mutant versus wild type NAC in order to determine the influence of the mutated motive on the structural dynamics of NAC.

2019-07-25 | PXD011995 | Pride

The ubiquitin-like modifier FAT10 interferes with SUMO activation

Project description:In this study, the proteins SumoE1 and Fat10 or Fat10-AV mutant were crosslinked using the crosslinking reagent H12/D12 BS3 in order to determine specific interaction sites of Fat10 and SumoE1. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-XL-MS) was used to compare crosslink abundances of SumoE1 in presence of Sumo as well as Sumo and Fat10 versus crosslink abundances of SumoE1 in absence of Sumo and Fat10 in order to determine the influence of Sumo and Fat10 on the structural dynamics of SumoE1.

2019-10-08 | PXD012592 | Pride